LncMAP: Pan-cancer Atlas of Long Noncoding RNA-mediated Transcriptional Network Perturbations

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2018 Jan 12

PMID 29325141

Citations 66

Authors

Yongsheng Li

Lili Li

Zishan Wang

Tao Pan

Nidhi Sahni

Xiyun Jin

Guangjuan Wang

Junyi Li

Xiangyi Zheng

Yunpeng Zhang

Juan Xu

Song Yi

Xia Li

Affiliations

Soon will be listed here.

Abstract

Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional perturbations remain a fundamental challenge for cancer biology. We show that transcriptional perturbations are widely mediated by long noncoding RNAs (lncRNAs) via integration of genome-wide transcriptional regulation with paired lncRNA and gene expression profiles. Systematic construction of an LncRNA Modulator Atlas in Pan-cancer (LncMAP) reveals distinct types of lncRNA regulatory molecules, which are expressed in multiple tissues, exhibit higher conservation. Strikingly, cancers with similar tissue origin share lncRNA modulators which perturb the regulation of cell cycle and immune response-related functions. Furthermore, we identified a large number of pan-cancer lncRNA modulators with potential clinical significance, which are differentially expressed in cancer or are strongly correlated with drug sensitivity across cell lines. Further stratification of cancer patients based on lncRNA-mediated transcriptional perturbations identifies subtypes with distinct survival rates. Finally, we made a user-friendly web interface available for exploring lncRNA-mediated transcriptional perturbations across cancer types. Our study provides a systems-level dissection of lncRNA-mediated regulatory perturbations in cancer, and also presents a valuable tool and resource for investigating the function of lncRNAs in cancer.

Citing Articles

Computational Resources for lncRNA Functions and Targetome.

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Yin J, Ding N, Yu J, Wang Z, Fu L, Li Y Mol Ther Nucleic Acids. 2023; 34:102058.

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Yu H, Zhang B, Qi L, Han J, Guan M, Li J PeerJ. 2023; 11:e15937.

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